Thanks for the fast answer. I will run more tests.
I think the bit-perfect capturing is 99,9% safe, but I will try to capture an AC3 Laserdisc (Shame on me, I don't have a DTS Laserdisc).
But the problem is 100% not the analog way of capturing.
When I capture a CD from my Blu-ray player via Toslink, it's the same phenomenon.
The captured WAV via Toslink is shorter than the 1:1 ripped Data WAV from the CD.
That is the ultimate proof that something went wrong during the digital capturing process.
The question is what really went wrong!? Maybe someone here has the same audio card and could also run a test!?